cBioportal Boxplot: GE ~ Clinical TCGA
Communication
- Visualize and test association between clinical data with gene expression (z-scores)
- p-values are results of Welch’s t.test between two groups of expression
z-scores larger than 6 are capped to 6, for better visualization
- Database: CBioportal
- cancer: Breast Cancer
- subset: Breast Cancer Breast Invasive Carcinoma (TCGA, Cell 2015), brca_tcga_pub2015_all, 818 samples
expression profile: brca_tcga_pub2015_rna_seq_v2_mrna_median_Zscores
All files could be downloaded from here.
Load Expression Data
## [1] "study: brca_tcga_pub2015"## [1] "case: brca_tcga_pub2015_all"## [1] "profile: brca_tcga_pub2015_rna_seq_v2_mrna_median_Zscores"Overview of Expression Data
## [1] "set outliers with expression > 6 to 6"## [1] "num ourliers before capping:" "14"## [1] "num ourliers after capping:" "0"
Load Clinical Data
##
## Others TNBC
## 621 51Plotting
TNBC
## [1] "Number of samples for TNBC"
##
## Others TNBC
## 621 51
## [1] "Welch's t.test was used for p-value calculation"
## [1] "comparison: " "Others" "TNBC"
ER_STATUS_BY_IHC
## [1] "Number of samples for ER_STATUS_BY_IHC"
##
## Indeterminate Negative Positive
## 2 175 601
## [1] "Welch's t.test was used for p-value calculation"
## [1] "comparison: " "Positive" "Negative"
HER2_FISH_STATUS
## [1] "Number of samples for HER2_FISH_STATUS"
##
## Indeterminate Negative Positive
## 3 247 60
## [1] "Welch's t.test was used for p-value calculation"
## [1] "comparison: " "Positive" "Negative"
PR_STATUS_BY_IHC
## [1] "Number of samples for PR_STATUS_BY_IHC"
##
## Indeterminate Negative Positive
## 4 251 522
## [1] "Welch's t.test was used for p-value calculation"
## [1] "comparison: " "Positive" "Negative"
Multiple Groups
TUMOR_STAGE
## [1] "Passed Levene's test(data not shown), perform ANOVA"## [1] "Number of samples for AJCC_PATHOLOGIC_TUMOR_STAGE"##
## I IA IB II IIA IIB III IIIA IIIB IIIC IV X
## 75 60 5 3 269 190 2 112 22 48 13 10## [1] "Welch t.test was used for p-value calculation to add * to the plot"## [1] "ref is I"
## [1] "ANOVA: not significant"## [1] "Pair-wise comparisons: some significant pair-wise comparisons at the p-value level, at p.adj (holm) no comparison is significant"## .y. group1 group2 p p.adj p.format p.signif method
## 1 SEPHS2 IIA IB 0.037326351 1.00 0.0373 * T-test
## 2 SEPHS2 IIB IB 0.041083736 1.00 0.0411 * T-test
## 3 SEPHS2 IIIA IB 0.020917058 1.00 0.0209 * T-test
## 4 SEPHS2 IV IB 0.017876938 1.00 0.0179 * T-test
## 5 SEPHS2 IB IIIB 0.026430262 1.00 0.0264 * T-test
## 6 SLC7A11 I IIA 0.034594351 1.00 0.0346 * T-test
## 7 SLC7A11 IIA IA 0.029578456 1.00 0.0296 * T-test
## 8 SLC7A11 IIA IV 0.007058173 0.47 0.0071 ** T-test
## 9 SLC7A11 IIA X 0.027349097 1.00 0.0273 * T-test
## 10 SLC7A11 IIA III 0.022970266 1.00 0.0230 * T-test
## 11 SLC7A11 IIIB III 0.035691849 1.00 0.0357 * T-testCANCER_TYPE_DETAILED
## [1] "Levene's test failed, ANOVA assumption not met, only perform pair-wise Welch's T.test"## [1] "Number of samples for CANCER_TYPE_DETAILED"##
## Breast Invasive Ductal Carcinoma
## 490
## Breast Invasive Lobular Carcinoma
## 127
## Breast Mixed Ductal and Lobular Carcinoma
## 88
## Invasive Breast Carcinoma
## 113## [1] "Welch's t.test was used for p-value calculation"## [1] "Welch t.test was used for p-value calculation to add * to the plot"## [1] "ref is Breast Invasive Lobular Carcinoma"
## [1] "Pair-wise comparisons: all significant pair-wise comparisons at the p-value level listed, at p.adj (holm) some comparison is significant"## .y. group1
## 1 PSTK Breast Invasive Ductal Carcinoma
## 2 SCLY Breast Invasive Lobular Carcinoma
## 3 SEPHS2 Invasive Breast Carcinoma
## 4 SEPHS2 Breast Invasive Ductal Carcinoma
## 5 SEPHS2 Breast Invasive Lobular Carcinoma
## 6 SEPSECS Invasive Breast Carcinoma
## 7 SEPSECS Invasive Breast Carcinoma
## 8 SEPSECS Breast Invasive Ductal Carcinoma
## 9 SEPSECS Breast Invasive Ductal Carcinoma
## 10 SLC7A11 Invasive Breast Carcinoma
## 11 SLC7A11 Breast Invasive Ductal Carcinoma
## 12 SLC7A11 Breast Invasive Lobular Carcinoma
## group2 p p.adj p.format
## 1 Breast Mixed Ductal and Lobular Carcinoma 1.648492e-02 9.9e-02 0.01648
## 2 Breast Mixed Ductal and Lobular Carcinoma 2.104185e-02 1.3e-01 0.02104
## 3 Breast Invasive Lobular Carcinoma 1.063428e-04 4.3e-04 0.00011
## 4 Breast Invasive Lobular Carcinoma 1.606515e-18 9.6e-18 < 2e-16
## 5 Breast Mixed Ductal and Lobular Carcinoma 2.394450e-05 1.2e-04 2.4e-05
## 6 Breast Invasive Lobular Carcinoma 4.158010e-02 1.2e-01 0.04158
## 7 Breast Mixed Ductal and Lobular Carcinoma 6.986600e-03 2.8e-02 0.00699
## 8 Breast Invasive Lobular Carcinoma 2.106862e-03 1.1e-02 0.00211
## 9 Breast Mixed Ductal and Lobular Carcinoma 7.956582e-04 4.8e-03 0.00080
## 10 Breast Invasive Lobular Carcinoma 2.227005e-02 8.9e-02 0.02227
## 11 Breast Invasive Lobular Carcinoma 8.874273e-06 5.3e-05 8.9e-06
## 12 Breast Mixed Ductal and Lobular Carcinoma 1.537631e-02 7.7e-02 0.01538
## p.signif method
## 1 * T-test
## 2 * T-test
## 3 *** T-test
## 4 **** T-test
## 5 **** T-test
## 6 * T-test
## 7 ** T-test
## 8 ** T-test
## 9 *** T-test
## 10 * T-test
## 11 **** T-test
## 12 * T-test